Please understand that your science captain would not have to fly a science ship and can fly an escort.

Agreed. I run sci captains on both KDF and Fed sides, both in escort-class ships. You do not need to rely on Sci BO abilities for primary damage. Instead, use tactical BO skills like cannon rapid fire, high yield torpedo, or whatever matches your chosen ship weapons load-out to deal damage, and sci abilities like tractor beam, jam sensors, sub-nuc, etc... to control and cripple your opponents. Rather than using brute force to overwhelm their targets, sci captains rely on debuffs to bypass their defenses.